I still can't figure out why this isn't baked into the Evernote application as a Service available system-wide, but there's a way to add a Service to send messages from Mail into Evernote as notes for archive. There was a previous applescript solution, but I hadn't used it (and it apparently borked on the 10.9 upgrade anyway).
I'd been using the Evernote email address feature, to just forward messages I need to archive for automatic importing into Evernote, but it's a pain. I have to remove the *FWD: * prefix on the note title. I need to decrease the indented quote level of messages. etc… It works, but it's funky.
Some quick searching turned up this post on the Evernote website. It talks about using an Automator app as a GTD workflow. Awesome. Except the app they provide includes a step to move archived messages into an "Archive" mailbox in Mail. I don't want to do that, so I modified the app ever so slightly, to remove that step.
Now, I have it set up as a Service, and have followed the instructions on the Evernote post to add a keyboard shortcut. Command-option-E sends selected message(s) to Evernote. Done. Awesome.
Here's my modified Automator app - download the .zip, extract it, and double-click on the app inside. It'll ask you if you want to install it. If you haven't already turned off the "Allow Apps from Anywhere" setting, you'll get a warning saying that you haven't done so. Easy fix. Open System Preferences, click "Security & Privacy" and then click the lock at the bottom left. Then, click "Allow apps downloaded from: anywhere". Done.
The one wrinkle I've seen so far is that the current version doesn't pull attachments over. That sucks. Attachments are one of the reasons I archive stuff. Looking into solutions for that now…